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ParserSupport.AbstractConsumer --+ | _BaseGenBankConsumer --+ | _FeatureConsumer
Create a SeqRecord object with Features to return.
Attributes: o use_fuzziness - specify whether or not to parse with fuzziness in feature locations. o feature_cleaner - a class that will be used to provide specialized cleaning-up of feature values.
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Inherited from Inherited from Inherited from |
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Inherited from |
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Set the accession number as the id of the sequence. If we have multiple accession numbers, the first one passed is used. |
Set the version to overwrite the id. Since the verison provides the same information as the accession number, plus some extra info, we set this as the id if we have a version. |
Attempt to determine the sequence region the reference entails. Possible types of information we may have to deal with: (bases 1 to 86436) (sites) (bases 1 to 105654; 110423 to 111122) 1 (residues 1 to 182) |
Get reference locations out of a string of reference information The passed string should be of the form: 1 to 20; 20 to 100 This splits the information out and returns a list of location objects based on the reference locations. |
Utility function to add a feature to the SeqRecord. This does all of the appropriate checking to make sure we haven't left any info behind, and that we are only adding info if it exists. |
Parse out location information from the location string. This uses Andrew's nice spark based parser to do the parsing for us, and translates the results of the parse into appropriate Location objects. |
Set the location information based on a function. This handles all of the location functions like 'join', 'complement' and 'order'. Arguments: o function - A LocationParser.Function object specifying the function we are acting on. o cur_feature - The feature to add information to. |
Parse a join or order and all of the information in it. This deals with functions that order a bunch of locations, specifically 'join' and 'order'. The inner locations are added as subfeatures of the top level feature |
Set the location information for a feature from the parse info. Arguments: o parse_info - The classes generated by the LocationParser. o cur_feature - The feature to add the information to. |
Set the location information for a feature. Arguments: o location - An AbsoluteLocation object specifying the info about the location. o cur_feature - The feature to add the information to. |
Return a (possibly fuzzy) location from a Range object. Arguments: o range_info - A location range (ie. something like 67..100). This may also be a single position (ie 27). This returns a FeatureLocation object. If parser.use_fuzziness is set at one, the positions for the end points will possibly be fuzzy. |
Return a (possibly fuzzy) position for a single coordinate. Arguments: o position - This is a LocationParser.* object that specifies a single coordinate. We will examine the object to determine the fuzziness of the position. This is used with _get_location to parse out a location of any end_point of arbitrary fuzziness. |
Add a qualifier to the current feature without loss of info. If there are multiple qualifier keys with the same name we would lose some info in the dictionary, so we append a unique number to the end of the name in case of conflicts. |
When we get a qualifier key, use it as a dictionary key. We receive a list of keys, since you can have valueless keys such as /pseudo which would be passed in with the next key (since no other tags separate them in the file) |
Add up sequence information as we get it. To try and make things speedier, this puts all of the strings into a list of strings, and then uses string.join later to put them together. Supposedly, this is a big time savings |
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